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tschuelia / PyPythia

Lightweight python library for predicting the difficulty of alignments in phylogenetics
GNU General Public License v3.0
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Option to clean up the temporary files #5

Closed BenoitMorel closed 2 years ago

BenoitMorel commented 2 years ago

Hi again ;-) I have run PyThia on several large datasets (with many alignments), and ended up filling my disc with temporary files. Since the user is not really aware of those files, maybe PyThia could remove them, either optionally or by default?

tschuelia commented 2 years ago

Hi :D that is a bit odd, I'm using the python tempfile module, which (according to the documentation) does the cleanup. What kind of temporary files are still present? The RAxML-NG files or temporary MSAs?

BenoitMorel commented 2 years ago

After one run on phobos:

ls /tmp/*raxml*
/tmp/tmpa6y_x2ug.raxml.log  /tmp/tmpa6y_x2ug.raxml.rfDistances  /tmp/tmpvibtcxjj.raxml.log  /tmp/tmpvibtcxjj.raxml.rba  /tmp/tmpvibtcxjj.raxml.startTree

Maybe they are removed after several minutes/hours? I have been running the tool on many files in a very short period of time.

tschuelia commented 2 years ago

tempfile should do the clean up immediately when the context ends turns out I made a mistake, but it should be fixed now ;-)

BenoitMorel commented 2 years ago

Yes, it's fixed. Thanks for fixing all the issues to quickly :-)